R/DAISIE_sim_constant_rate_shift.R

In xieshu95/DAISIE_new: Dynamical Assembly of Islands by Speciation, Immigration and Extinction

#' @title Simulate islands with given parameters.
#' @description This function simulates islands with given cladogenesis,
#' extinction, Kprime, immigration and anagenesis parameters. If a single
#' parameter set is provided (5 parameters) it simulates islands where all
#' species have the same macro-evolutionary process. If two paramater sets
#' (10 parameters) are provided, it simulates islands where two different
#' macro-evolutionary processes operate, one applying to type 1 species and
#' other to type 2 species. If two parameter sets and a time shift (11
#' parameters) are provided, it simulates islands where at the given time
#' a shift between the parameter sets will occur.
#'
#' Returns R list object that contains the simulated islands
#'
#' @inheritParams default_params_doc
#'
#' @return Each simulated dataset is an element of the list, which can be
#' called using [[x]]. For example if the object is called island_replicates,
#' the last replicates is a list in itself. The first (e.g.
#' island_replicates[[x]][[1]]) element of that list has the following
#' components: \cr \code{$island_age} - the island age \cr Then, depending on
#' whether a distinction between types is made, we have:\cr \code{$not_present}
#' - the number of mainland lineages that are not present on the island \cr
#' or:\cr \code{$not_present_type1} - the number of mainland lineages of type 1
#' that are not present on the island \cr \code{$not_present_type2} - the
#' number of mainland lineages of type 2 that are not present on the island \cr
#' \code{$stt_all} - STT table for all species on the island (nI - number of
#' non-endemic species; nA - number of anagenetic species, nC - number of
#' cladogenetic species, present - number of independent colonisations present
#' )\cr \code{$stt_stt_type1} - STT table for type 1 species on the island -
#' only if 2 types of species were simulated (nI - number of non-endemic
#' species; nA - number of anagenetic species, nC - number of cladogenetic
#' species, present - number of independent colonisations present )\cr
#' \code{$stt_stt_type2} - STT table for type 2 species on the island - only if
#' 2 types of species were simulated (nI - number of non-endemic species; nA -
#' number of anagenetic species, nC - number of cladogenetic species, present -
#' number of independent colonisations present )\cr \code{$brts_table} - Only
#' for simulations under 'IW'. Table containing information on order of events
#' in the data, for use in maximum likelihood optimization.)\cr
#'
#' The subsequent elements of the list each contain information on a single
#' colonist lineage on the island and has 4 components:\cr
#' \code{$branching_times} - island age and stem age of the population/species
#' in the case of Non-endemic, Non-endemic_MaxAge and Endemic anagenetic
#' species. For cladogenetic species these should be island age and branching
#' times of the radiation including the stem age of the radiation.\cr
#' \code{$stac} - the status of the colonist \cr * Non_endemic_MaxAge: 1 \cr *
#' ndemic: 2 \cr * Endemic&Non_Endemic: 3 \cr * Non_endemic: 4 \cr
#' \code{$missing_species} - number of island species that were not sampled for
#' particular clade (only applicable for endemic clades) \cr \code{$type_1or2}
#' - whether the colonist belongs to type 1 or type 2 \cr
#' @author Luis Valente and Albert Phillimore
#' @seealso \code{\link{DAISIE_format_CS}} \code{\link{DAISIE_plot_sims}}
#' @references Valente, L.M., A.B. Phillimore and R.S. Etienne (2015).
#' Equilibrium and non-equilibrium dynamics simultaneously operate in the
#' Galapagos islands. Ecology Letters 18: 844-852.
#' Hauffe, T., D. Delicado, R.S. Etienne and L. Valente (submitted).
#' Lake expansion increases equilibrium diversity via the target effect of
#' island biogeography.
#' @keywords models
#' @export
DAISIE_sim_constant_rate_shift <- function(
  time,
  M,
  pars,
  replicates,
  divdepmodel = "CS",
  nonoceanic_pars = c(0, 0),
  num_guilds = NULL,
  sample_freq = 25,
  plot_sims = TRUE,
  hyper_pars = NULL,
  area_pars = NULL,
  dist_pars = NULL,
  shift_times = NULL,
  verbose = TRUE,
  ...
) {
  testit::assert(
    "length(pars) is not ten and/or shift_times is not null,
    set ten parameters with non-null shift_times",
    length(pars) == 10 && !is.null(shift_times)
  )

  totaltime <- time
  island_replicates <- list()
  if (divdepmodel == "IW") {
    for (rep in 1:replicates) {
      island_replicates[[rep]] <- DAISIE_sim_core_constant_rate_shift(
        time = totaltime,
        mainland_n = M,
        pars = pars,
        nonoceanic_pars = nonoceanic_pars,
        hyper_pars = hyper_pars,
        area_pars = area_pars,
        dist_pars = dist_pars,
        shift_times = shift_times
      )
      if (verbose == TRUE) {
        print(paste("Island replicate ", rep, sep = ""))
      }
    }
    island_replicates <- DAISIE_format_IW(island_replicates = island_replicates,
                                          time = totaltime,
                                          M = M,
                                          sample_freq = sample_freq,
                                          verbose = verbose)
  }
  if (divdepmodel == "CS") {
      for (rep in 1:replicates) {
        island_replicates[[rep]] <- list()
        full_list <- list()
        for (m_spec in 1:M) {
          full_list[[m_spec]] <- DAISIE_sim_core_constant_rate_shift(
            time = totaltime,
            mainland_n = 1,
            pars = pars,
            nonoceanic_pars = nonoceanic_pars,
            hyper_pars = hyper_pars,
            area_pars = area_pars,
            dist_pars = dist_pars,
            shift_times = shift_times
          )
        }
        island_replicates[[rep]] <- full_list
        if (verbose == TRUE) {
          print(paste("Island replicate ", rep, sep = ""))
        }
      }
    island_replicates <- DAISIE_format_CS(
      island_replicates = island_replicates,
      time = totaltime,
      M = M,
      sample_freq = sample_freq,
      verbose = verbose
    )
  }

  if (divdepmodel == "GW") {
    if (!is.numeric(num_guilds)) {
      stop("num_guilds must be numeric")
    }
    guild_size <- M / num_guilds
    testit::assert(num_guilds < M)
    testit::assert(M %% num_guilds == 0)
    for (rep in 1:replicates) {
      island_replicates[[rep]] <- list()
      full_list <- list()
      for (m_spec in 1:num_guilds) {
        full_list[[m_spec]]  <- DAISIE_sim_core_constant_rate_shift(
          time = totaltime,
          mainland_n = guild_size,
          pars = pars,
          nonoceanic_pars = nonoceanic_pars,
          hyper_pars = hyper_pars,
          area_pars = area_pars,
          dist_pars = dist_pars,
          shift_times = shift_times
        )
      }
      island_replicates[[rep]] <- full_list
      if (verbose == TRUE) {
        print(paste("Island replicate ", rep, sep = ""))
      }
    }
    island_replicates <- DAISIE_format_GW(island_replicates = island_replicates,
                                          time = totaltime,
                                          M = M,
                                          sample_freq = sample_freq,
                                          num_guilds = num_guilds,
                                          verbose = verbose)
  }
  if (plot_sims == TRUE) {
    DAISIE_plot_sims(
      island_replicates = island_replicates,
      sample_freq = sample_freq
    )
  }
  return(island_replicates)
}